Transforming a cube to a sphere using transform to sphere isn't creating a sphere it creates a spike shaped mesh
There may be a scaling issue here. If you take a cube and:


In edit mode, subdivide it
In object mode, scale it along one axis
Back in edit mode scale it back down the axis so it looks like a cube again
And then use ShiftAltS .. 'To Sphere'


...you wind up with a similar result to yours.

In short, in object mode, CtrlA apply any scale that might be locked into the object's transform matrix.

If ever you make a non-uniform scale of something in Object Mode.. make a mental note of it, and/or keep an eye on the Transform panel in the Properties Region of the 3D view (in Object Mode). You may need to go back and bake the transform into the mesh by applying it.